The difference is that the Great Wheel is a mostly-closed cosmology. There are exactly 17 outer planes and they are defined by alignments. Since alignments are a bad idea and should not be part of anything at all, I don't like that. The World Axis, on the other hand, says "Here's the Astral Sea, and within that you'll find all sorts of planes. Some, but not all, are homes to gods. Some have weird cosmic phenomena. Some look much like the world you're from, others look entirely different." That leaves a lot more room for fun stuff.
I mean, just look at all the weird dimensions that have popped up in various Marvel comics over the years. That's what I want in a cosmology, not mindless box-checking.